version update

doc/source/cli.rst

@@ -86,7 +86,9 @@ Settings explained:
 |               |                                 | indexes to map to |
 +---------------+---------------------------------+-------------------+
 | features      | Homo_sapiens.GRCh37.75.gtf      | genome annotation |
-|               |                                 | file              |
+|               |                                 | file. ONLY needed |
+|               |                                 | for counting      |
+|               |                                 | genomic features  |
 +---------------+---------------------------------+-------------------+
 | output        | smrna_results                   | output folder for |
 |               |                                 | temp files        |

doc/source/description.rst

@@ -84,6 +84,10 @@ Then finally run::
 
   pip install smallrnaseq
 
+Or for the current github version you can use::
+
+  pip install -e git+https://github.com/dmnfarrell/smallrnaseq.git#egg=smallrnaseq
+
 Snap package
 ++++++++++++
 

setup.py

@@ -18,7 +18,7 @@
 
 setup(
     name = 'smallrnaseq',
-    version = '0.5.0',
+    version = '0.6.0',
     description = 'Package for short RNA-seq analysis',
     long_description = 'smallrnaseq is a Python package for processing of small RNA seq data.',
     url='https://github.com/dmnfarrell/smallrnaseq',

smallrnaseq/__init__.py

@@ -1,4 +1,4 @@
 from .base import *
 from .utils import *
 #from analysis import *
-__version__ = '0.5.0'
+__version__ = '0.6.0'

smallrnaseq/app.py

@@ -511,6 +511,9 @@ def main():
                         default=False, help="run DE analysis")
     parser.add_option("-t", "--tests", dest="tests",  action="store_true",
                         default=False, help="run tests")
+    parser.add_option("-v", "--version", dest="version", action="store_true",
+                        help="Get version")
+
     opts, remainder = parser.parse_args()
 
     if opts.infile != None:
@@ -545,6 +548,9 @@ def main():
             print_help()
     elif opts.tests == True:
         test_run()
+    elif opts.version == True:
+        from . import __version__
+        print ('smallrnaseq version %s' %__version__)        
     else:
         if opts.config != None:
             conffile = opts.config